Hi Farzin,

In this answer I am assuming you are using is a non specific fluorescent dye that interacts with all double stranded DNA.

-If it's truly primer dimer you should see the peak in no patient input DNA controls as well, Is this the case?

If not it indicates this is somehow being templated by the patient DNA

-That you see it in only some patient samples would be consistent with primer dimer as the cause only if there is differences in the level of input of target DNA.

If a large number of target molecules are present the primers are preferentially used for target amplification. Also, if you are using a non saturating dye (such as sybr green) the dye available will be essentially used up by the large amount of target amplicon present, masking the presence of the lower temperature melting product.

For high resolution melt analysis saturating dyes are necessary. The melt curve will not be shifted nor primer dimers hidden. They can be used at saturating concentrations because they are not toxic to Taq (sybr green is at higher concentrations). I have had good luck with Syto9, but there are several available listed at this site;

https://www.gene-quantification.de/hrm-dyes.html

Hope this was helpful.

Frank

...another approach to prevent or reduce PD formation is by modifying the primers so that annealing with themselves or each other does not cause extension. HANDS (Homo-Tag Assisted Non-Dimer System): a nucleotide tail, complementary to the 3' end of the primer is added to the 5' end of the primer. https://en.m.wikipedia.org/wiki/Primer_dimer

Check https://data.epo.org/publication-server/rest/v1.0/publication-dates/20180829/patents/EP3134554NWB1/document.pdf

https://www.jmdjournal.org/article/S1525-1578(14)00003-8/fulltext